Package: rGREAT 2.7.0

Zuguang Gu

rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions

GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.

Authors:Zuguang Gu [aut, cre]

rGREAT_2.7.0.tar.gz
rGREAT_2.7.0.zip(r-4.5)rGREAT_2.7.0.zip(r-4.4)rGREAT_2.7.0.zip(r-4.3)
rGREAT_2.7.0.tgz(r-4.4-arm64)rGREAT_2.7.0.tgz(r-4.4-x86_64)rGREAT_2.7.0.tgz(r-4.3-arm64)rGREAT_2.7.0.tgz(r-4.3-x86_64)
rGREAT_2.7.0.tar.gz(r-4.5-noble)rGREAT_2.7.0.tar.gz(r-4.4-noble)
rGREAT_2.7.0.tgz(r-4.4-emscripten)rGREAT_2.7.0.tgz(r-4.3-emscripten)
rGREAT.pdf |rGREAT.html✨
rGREAT/json (API)
NEWS

# Install 'rGREAT' in R:
install.packages('rGREAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jokergoo/rgreat/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:rGREAT-2.7.0(bioc 3.20)rGREAT-2.6.0(bioc 3.19)

bioconductor-package

32 exports 2.00 score 113 dependencies 2 dependents 5 mentions

Last updated 2 months agofrom:a6da6b1fe9

Exports:availableCategoriesavailableOntologiesextendTSSextendTSSFromDataFrameextendTSSFromOrgDbextendTSSFromTxDbgetEnrichmentTablegetEnrichmentTablesgetGapFromUCSCgetGeneSetsFromBioMartgetGeneSetsFromOrgDbgetGenesFromGencodegetGenomeDataFromNCBIgetGREATDefaultTSSgetKEGGGenomegetKEGGPathwaysgetRefSeqGenesFromUCSCgetRegionGeneAssociationsgetTSSgreatgreat_optGreatJobGreatObjectplotRegionGeneAssociationGraphsplotRegionGeneAssociationsplotVolcanorandomRegionsrandomRegionsFromBioMartGenomeread_gmtreduce_by_start_and_endshinyReportsubmitGreatJob

Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemcirclizeclicodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurlDBIDelayedArraydigestdoParallelDTevaluatefastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongGlobalOptionsglueGO.dbhighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesiteratorsjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngprettyunitsprogresspromisesR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassshapeshinysnowsourcetoolsSparseArraySummarizedExperimentsystinytexTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsvctrswithrxfunXMLxtableXVectoryamlzlibbioc

The rGREAT package

Zuguang Gu ([email protected])

Rendered fromrGREAT.Rmdusingknitr::rmarkdownon Jun 15 2024.

Last update: 2024-02-27
Started: 2015-02-13

Readme and manuals

Help Manual

Help pageTopics
Available ontology categories of the GREAT jobavailableCategories availableCategories,GreatJob-method
All available ontology names of the GREAT jobavailableOntologies availableOntologies,GreatJob-method
Extend TSSextendTSS
Extend TSSextendTSSFromDataFrame
Extend TSSextendTSSFromOrgDb
Extend TSSextendTSSFromTxDb
Method dispatch page for getEnrichmentTablegetEnrichmentTable
Get a single enrichment table from GREAT web servergetEnrichmentTable,GreatJob-method
Get enrichment tablegetEnrichmentTable,GreatObject-method
Method dispatch page for getEnrichmentTablesgetEnrichmentTables
Get enrichment tables from GREAT web servergetEnrichmentTables,GreatJob-method
Get enrichment tablegetEnrichmentTables,GreatObject-method
Get gap regions from UCSCgetGapFromUCSC
Get GO gene sets from BioMartgetGeneSetsFromBioMart
Get GO gene sets from OrgDb objectgetGeneSetsFromOrgDb
Get Gencode genesgetGenesFromGencode
Get genome data from NCBIgetGenomeDataFromNCBI
Get built-in TSS from GREATgetGREATDefaultTSS
Get the corresponding assembly id for a kegg organismgetKEGGGenome
Get KEGG pathway gene setsgetKEGGPathways
Get RefSeq genes from UCSCgetRefSeqGenesFromUCSC
Method dispatch page for getRegionGeneAssociationsgetRegionGeneAssociations
Get region-gene associationsgetRegionGeneAssociations,GreatJob-method
Get region-gene associationsgetRegionGeneAssociations,GreatObject-method
Get the internally used TSSgetTSS
Perform GREAT analysisgreat
Global parameters for rGREATgreat_opt
Constructor method for GreatJob classGreatJob
Class to store and retrieve GREAT resultsGreatJob-class
Constructor method for GreatObject classGreatObject
Class for local GREAT analysisGreatObject-class
Plot region-gene associationsplotRegionGeneAssociationGraphs plotRegionGeneAssociationGraphs,GreatJob-method
Method dispatch page for plotRegionGeneAssociationsplotRegionGeneAssociations
Plot region-gene associationsplotRegionGeneAssociations,GreatJob-method
Plot region-gene associationsplotRegionGeneAssociations,GreatObject-method
Method dispatch page for plotVolcanoplotVolcano
Make volcano plotplotVolcano,GreatJob-method
Make volcano plotplotVolcano,GreatObject-method
Generate random regionsrandomRegions
Generate random regions from a BioMart genomerandomRegionsFromBioMartGenome
Read gmt gene sets fileread_gmt
Reduce by start and endreduce_by_start_and_end
Method dispatch page for shinyReportshinyReport
Shiny app on the GreatJob objectshinyReport,GreatJob-method
Shiny app on the GreatObject objectshinyReport,GreatObject-method
Perform online GREAT analysissubmitGreatJob